6E9D

Sub-2 Angstrom Ewald Curvature-Corrected Single-Particle Cryo-EM Reconstruction of AAV-2 L336C


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Sub-2 angstrom Ewald curvature corrected structure of an AAV2 capsid variant.

Tan, Y.Z.Aiyer, S.Mietzsch, M.Hull, J.A.McKenna, R.Grieger, J.Samulski, R.J.Baker, T.S.Agbandje-McKenna, M.Lyumkis, D.

(2018) Nat Commun 9: 3628-3628

  • DOI: https://doi.org/10.1038/s41467-018-06076-6
  • Primary Citation of Related Structures:  
    6E9D

  • PubMed Abstract: 

    Single-particle cryogenic electron microscopy (cryo-EM) provides a powerful methodology for structural biologists, but the resolutions typically attained with experimentally determined structures have lagged behind microscope capabilities. Here, we exploit several technical advances to improve resolution, including per-particle contrast transfer function (CTF) refinement and correction for Ewald sphere curvature. The latter is demonstrated with several experimental samples and should become more standard as resolutions increase or at lower microscope accelerating voltages. The combined application of the described methods to micrographs recorded on a Titan Krios enables structure determination at ~1.86-Å resolution of an adeno-associated virus serotype 2 variant (AAV2), an important gene-delivery vehicle. The resulting structural details provide an improved model for understanding the biology of AAV that will guide future vector development for gene therapy.


  • Organizational Affiliation

    The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY, 10027, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP1735Adeno-associated virus 2 Srivastava/1982Mutation(s): 1 
Gene Names: VP1
UniProt
Find proteins for P03135 (Adeno-associated virus 2 (isolate Srivastava/1982))
Explore P03135 
Go to UniProtKB:  P03135
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03135
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13
RECONSTRUCTIONFREALIGN9.11

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI136680-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM109524
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM033050

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-09-19
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2020-02-26
    Changes: Source and taxonomy
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Refinement description